1731 commits

Author	SHA1	Message	Date
JIANHONG OU	fadb83cf44	Merge branch 'master' into motus_profile	2022-05-13 09:30:20 -04:00
Matthias De Smet	cbc47767f7	add sort option to bowtie2	2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke	a72f06dfe8	removed versions checksum	2022-05-13 14:27:59 +02:00
nvnieuwk	1d4862ba60	Merge branch 'master' into new-module-gatk4/splitintervals	2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke	8a17b6dd0e	added gatk4/splitintervals	2022-05-13 13:46:34 +02:00
Chris Cheshire	ea55129ba3	Removed version file checksums	2022-05-13 12:20:41 +01:00
Chris Cheshire	9f6a1ae4a4	Merge branch 'master' into bowtie2-test-fix	2022-05-13 12:05:48 +01:00
Chris Cheshire	d816f2bc5d	Reactivated all tests	2022-05-13 12:01:16 +01:00
Taniguti	4728b2bcd2	Merge branch 'master' into haplocheck	2022-05-13 07:49:55 -03:00
Lucas Taniguti	c1ed4e21be	tests: add haplocheck tests	2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal	00826dc2e9	Merge branch 'master' into genomescope2	2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal	5df0bcf1be	Update tests/modules/genomescope2/test.yml ... Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>	2022-05-13 11:27:42 +02:00
James A. Fellows Yates	2eebab4f35	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
James A. Fellows Yates	8dd711aba2	Update tests/modules/motus/profile/main.nf	2022-05-12 20:08:37 +01:00
FriederikeHanssen	868150e1af	Merge branch 'master' into gatk_426	2022-05-12 19:33:07 +02:00
Rike	99880654bf	add output default bam	2022-05-12 18:06:15 +02:00
Rike	8792d102ee	fix test input	2022-05-12 17:37:06 +02:00
Rike	a694267b4b	fix empty index input	2022-05-12 17:01:03 +02:00
Mahesh Binzer-Panchal	308ab8801d	Merge branch 'master' into kat_hist	2022-05-12 16:52:05 +02:00
Rike	b3bd55da76	getpileupsummaries requires intervals files	2022-05-12 16:51:17 +02:00
Rike	15fbf21b28	double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere	2022-05-12 16:16:53 +02:00
Rike	fef5434c4c	Update md5sums	2022-05-12 16:07:12 +02:00
Jasmin F	85b3c2bcf2	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-12 15:28:19 +02:00
James A. Fellows Yates	3c02e6056c	Merge branch 'master' into antismashlite	2022-05-12 14:53:52 +02:00
Sateesh Peri	c5d3c90524	Merge branch 'master' into rp3-add-snippy	2022-05-12 07:48:33 -04:00
jasmezz	d2ef476321	Fix Prettier linting error	2022-05-12 12:19:50 +02:00
jasmezz	37cc6f250b	Fixed test.yml	2022-05-12 12:14:19 +02:00
Chris Cheshire	90c67794bf	Added extra tests but error with collection	2022-05-12 10:01:33 +01:00
jasmezz	bd4b70439b	Streamlined some output channels, formatted tests main.nf	2022-05-12 10:56:48 +02:00
Robert A. Petit III	8b6e1aff38	Merge branch 'master' into rp3-add-snippy	2022-05-11 12:28:27 -06:00
Robert A. Petit III	7ced6e20de	make prettier	2022-05-11 18:00:36 +00:00
Moritz E. Beber	74b11ccc44	refactor: rename and update subworkflow	2022-05-11 19:24:16 +02:00
Matthias De Smet	dcf9c07fc9	Merge branch 'master' into update/bowtie2-align	2022-05-11 19:08:23 +02:00
Moritz E. Beber	98d8a741ec	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
Moritz E. Beber	888620063b	tests: delete settings for conda	2022-05-11 17:44:49 +02:00
Moritz E. Beber	b2dbaa9930	refactor: rename module	2022-05-11 17:33:45 +02:00
Moritz E. Beber	23091aabda	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
Moritz E. Beber	a83dd33a7e	tests: use remove settings file	2022-05-11 17:33:45 +02:00
Moritz E. Beber	e4551a9ab3	refactor: always output settings	2022-05-11 17:33:45 +02:00
Moritz E. Beber	64ff23f3c1	feat: add module that verifies NCBI settings	2022-05-11 17:33:45 +02:00
Mahesh Binzer-Panchal	0199d0efd2	Merge branch 'master' into kat_hist	2022-05-11 16:56:29 +02:00
Harshil Patel	4e603393c3	Merge branch 'master' into update/bowtie2-align	2022-05-11 15:47:37 +01:00
Jasmin F	853e3ec087	Remove commented code ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-11 15:56:10 +02:00
Mahesh Binzer-Panchal	fbe2f85e7b	Fix path	2022-05-11 13:53:38 +00:00
Matthias De Smet	94e8c3a882	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:56:03 +02:00
Matthias De Smet	0d00452eca	Update tests/modules/bowtie2/align/test.yml ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2022-05-11 13:55:45 +02:00
Matthias De Smet	dcffd93875	Merge branch 'master' into update/bowtie2-align	2022-05-11 13:34:24 +02:00
CMGG ICT Team	3ae8cbfad7	bowtie2: remove code duplication	2022-05-11 13:32:56 +02:00
Moritz E. Beber	0cdf7767a7	refactor: require NCBI user settings always	2022-05-11 13:02:52 +02:00
Moritz E. Beber	eae7161a32	tests: add settings input or not and test all branches	2022-05-11 12:47:54 +02:00